Coincidentally, Python 2 had its final release just a few days ago. I
trust python components of CCP4 are all now using Python 3.
https://www.theregister.co.uk/2020/04/21/the_final_python_2_release/
-
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
------
On 2020-04-23 12:30, Eugene Krissinel wrote:
Dear CCP4 Users,
The CCP4 Core Group is very pleased to announce the release of the
latest version of the CCP4 Software Suite. Version 7.1 (Skipton) is
now available from the CCP4 download website
<http://www.ccp4.ac.uk/download.php>. The release is available for all
MS Windows, Linux and Mac OSX platforms.
Is it really necessary to switch to CCP4 7.1 now?
While CCP4 7.0 can be kept on your computers for as long as necessary
and in parallel to CCP4 7.1 (Mac OSX and Linux only), we encourage all
our users to switch over at first convenience because:
1. the release brings new, updated and improved components that make
structure solution with CCP4 yet more efficient and easy
2. the update line for CCP4 7.0 is now discontinued
3. support for CCP4 7.0, as well as for all earlier versions of CCP4,
is no longer available
CCP4 7.1 Release Highlights
CCP4 Release 7.1 comes as a complete modernisation of version 7.0,
which have seen the longest life time ever in CCP4 history, being
released more than 4 years ago and complemented with 79 updates.
However, changes in operating systems and advances in computer
languages, accumulated over this significant time period, have made it
necessary to introduce technical modifications, such as progressing to
C++-11, that could not be carried out using the CCP4 update system.
Main Updates and Improvements
CCP4 7.1 represents the final state of 7.0 update series, complemented
with newest versions of many important components, for example:
COOT 0.9
/The latest version of Interactive Model Building Software from Dr.
Paul Emsley, MRC/LMB, Cambridge, with many improvements and new features./
Currently available only for Mac OSX and Linux users. The
corresponding update for Windows systems will be issued as soon as
feasible
DIALS 2.1
/Diffraction image processing software from Diamond Light Source Ltd.,
CCP4 and the Lawrence Berkeley National Laboratory. DIALS now includes
a scaling module and improved multi-crystal symmetry tools./
DUI 2019.12
/A Graphical User Interface for DIALS programs./
XIA2 0.6.0
/Automated diffraction image processing using an expert system./
PHASER 2.8.3
/Maximum likelihood structure solution software from the group of
Prof. Randy Read, Cambridge./
SHELX
/SHELX Software from Prof. George Sheldrick, University of Goettingen,
Germany (SHELXE is supported by Dr. Isabel Uson, Barcelona, Spain)/
Buccaneer
/BUCCANEER Software from Dr. Kevin Cowtan, University of York, UK,
with important fixes and improvements/
and many others. CCP4 continues to provide
ARP/wARP 8.0
/Automated Model Building Software from Dr. Victor Lamzin, EMBL
Outstation in Hamburg, Germany/ integrated with the CCP4 Core package.
In CCP4 7.1, you will find considerably advanced and improved:
CCP4i2
/CCP4 Graphical Interface with many tasks and report pages revised and
partly redesigned, numerous bugs fixed and overall stability
enhanced./ In particular, CCP4i2 now contains the deposition module,
which allows you to prepare files in mmCIF format, suitable for
deposition to the PDB in a fairly automated manner.
New Software
In addition to numerous modifications, advances and updates, CCP4 7.1
introduces a few brand new components:
GEMMI
/C++/Python application and library for handling coordinate and
reflection data (from Marcin Wojdyr, Global Phasing Ltd., Cambridge, UK)/
GEMMI is a highly efficient and sophisticated package for manipulating
coordinate and reflection data in various formats (such as .pdb,
.mmcif, .mtz). The package is very useful for developing MX-related
applications in C++ and Python.
MRparse
/Assistant application for making and analysing search models for
Molecular Replacement (from the group of Prof. Daniel Rigden,
University of Liverpool, UK)/
MRparse finds suitable structure homologs, aligns and represents them
graphically for reference and more efficient MR ensembling. Available
in CCP4i2 interface.
CCP4 Cloud
/A framework for distributed CCP4 Computation/
CCP4 Cloud represents a conceptually new approach to organising and
maintaining crystallographic projects in CCP4 and running CCP4 tasks.
With this system, you can keep all your data and projects in the Cloud
and manage them using any modern browser running on a desktop PC,
laptop, tablet/ipad or even a smartphone, from any geographic
location. In CCP4 Cloud, only the initial data need to be uploaded
once; within a Project, the data is passed from task to task behind
the scenes, without exchange with the client device. CCP4 Cloud
represents Projects as branched trees, making the structure solution
pathway perfectly transparent and easily reconcilable. All main stages
of structure solution in MX: image processing, phasing, model
building, refinement, validation and PDB deposition are presented in
CCP4 Cloud as a collection of more than 75 tasks. Interactive tasks,
such as Coot, are also available in CCP4 Cloud. Using such tasks
requires a local CCP4 7.1 setup, which contains the CCP4 Cloud Client,
a piece of software linking CCP4 Cloud with Coot installed locally.
Just double-click on the CCP4 Cloud Client icon (CCP4 Diamond with a
cloud and wireless sign) in order to start using CCP4 Cloud right
after installation of CCP4 7.1 (you will be required to register as
CCP4 Cloud user first time).
The CCP4 Core Group will be happy to help anyone to start using CCP4
Cloud. Development of CCP4 Cloud was supported by BBSRC UK Grant
BB/L007037/1 and is a result of a collaborative effort of many
developers and enthusiasts.
CCP4build
/Automated model builder (from Eugene Krissinel and Andrey Lebedev,
CCP4 Core Group)/
CCP4build combines several applications: CParrot, CBuccaneer, Refmac,
Coot and EDStats, for the enhancement of automatic model building in
CCP4. CCP4build explores several model building scenarios in an
iterative approach with rollbacks, and adjusts automatically to
building in both experimental phases and phases obtained in the course
of molecular replacement. CCP4build is available in CCP4 Cloud.
BUSTER interface
/Interface to BUSTER software from Global Phasing Ltd./
The interface allows a user to refine macromolecular structures with
BUSTER software from Global Phasing Ltd. The interface is available
through the CCP4 Cloud - both in your own installation as well as
through the CCP4 Cloud service at RC Harwell (UK).
The latter case requires online authorisation for academic users with
Global Phasing Ltd. (which are kindly providing the software to all
academic users free of charge), which is done via an authorisation
facility found in user’s account settings. Use of the interface within
your local CCP4 Cloud installation requires a separate, local
installation from www.globalphasing.com <http://www.globalphasing.com>.
Technical notes
For Mac OSX and Linux platforms, on-line setup through the CCP4 Setup
Manager is the recommended option. CCP4 Setup Manager enables you to
choose a desirable set of components, download, install and configure
them automatically.
Before installing CCP4 7.1, PLEASE MAKE SURE THAT NO CCP4 PROGRAMS ARE
RUNNING, PARTICULARLY CCP4i AND CCP4i2. The simplest way to achieve
that is to REBOOT YOUR COMPUTER BEFORE THE INSTALLATION OF CCP4.
Installation on MS Windows systems requires downloading the whole
package as an executable installer and running it on your machine. Be
prepared to see a warning message from MS Windows, suggesting that the
software may be harmful for your system – please trust CCP4 and choose
“install anyway”. It is necessary that you REBOOT YOUR WINDOWS PC
AFTER INSTALLATION, before attempting to run any of CCP4 programs.
We advise you to always include Coot in your installation package and
install it simultaneously with the rest of CCP4. If you intend to use
Coot from other sources, be prepared to link it with CCP4 after
installation and manage it separately. CCP4 cannot provide updates to
Software installed from sources other than CCP4 and cannot guarantee a
flawless integration of such software – although we will do our best
in order to resolve any issues you may encounter.
Please note that, starting from CCP4 7.1, 32-bit packages are no
longer available.
Acknowledgements
We would like to thank all of the developers who have contributed to
CCP4 7.1, and all of those who have helped in testing it. The
following publication should be used to cite the use of CCP4:
M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P.
R. Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, S.
J. McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R.
Powell, R. J. Read, A. Vagin and K. S. Wilson (2011) /Overview of the
CCP4 suite and current developments/, Acta Cryst *D67* 235-242.
Use of individual CCP4 programs should be acknowledged also by the
citation of respective publications, where required (please cf. from
program documentation). CCP4 is supported by the BBSRC UK through
grant BB/S006974/1 (CCP4 Advanced Integrated Approaches to
Macromolecular Structure Determination), as well as by our industrial
users.
Final remarks
CCP4 7.1 is out now. A considerable effort has been put into
developing, compiling, bundling and testing its many new components
and underlying libraries. Despite all the effort we've made, bugs and
unforeseen “features” will most certainly be found in the Suite, which
has grown substantially in size. When bugs and errors are discovered,
the best way to deal with them is to report them to us at
c...@stfc.ac.uk <mailto:c...@stfc.ac.uk>. We value highly all feedback
from our users, and together we will bring CCP4 yet closer to
community expectations and standards.
Many thanks for being CCP4 users,
Eugene Krissinel
on behalf of CCP4 Core Group:
Charles Ballard
Andrey Lebedev
Ronan Keegan
David Waterman
Kyle Stevenson
Ville Uski
Oleg Kovalevskiy
Tarik Drevon
Karen McIntyre
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
-
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
